*** stack smashing detected ***: gffread terminated
dengyang111 opened this issue · comments
Hi, when i ran gffread, there was a bug.
How should id resolve it.
Thanks.
Code and bug info:
(m6A) [dengy@mu01 00_genome]$ gffread -T Ath_genomic.gff -o 1235
*** stack smashing detected ***: gffread terminated
======= Backtrace: =========
/usr/lib64/libc.so.6(__fortify_fail+0x37)[0x2ba7e179c6e7]
/usr/lib64/libc.so.6(+0x1186a2)[0x2ba7e179c6a2]
gffread(+0xf505)[0x562cba3be505]
gffread(+0x3a59)[0x562cba3b2a59]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ba7e16a6445]
gffread(+0x47e9)[0x562cba3b37e9]
======= Memory map: ========
2ba7e1460000-2ba7e1482000 r-xp 00000000 08:04 32118990 /usr/lib64/ld-2.17.so
2ba7e1482000-2ba7e1483000 rw-p 00000000 00:00 0
2ba7e1483000-2ba7e152c000 r--p 00000000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32
2ba7e152c000-2ba7e15cc000 r-xp 000a9000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32
2ba7e15cc000-2ba7e1653000 r--p 00149000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32
2ba7e1653000-2ba7e165e000 r--p 001cf000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32
2ba7e165e000-2ba7e1662000 rw-p 001da000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32
2ba7e1662000-2ba7e166f000 rw-p 00000000 00:00 0
2ba7e1681000-2ba7e1682000 r--p 00021000 08:04 32118990 /usr/lib64/ld-2.17.so
2ba7e1682000-2ba7e1683000 rw-p 00022000 08:04 32118990 /usr/lib64/ld-2.17.so
2ba7e1683000-2ba7e1684000 rw-p 00000000 00:00 0
2ba7e1684000-2ba7e1847000 r-xp 00000000 08:04 32118997 /usr/lib64/libc-2.17.so
2ba7e1847000-2ba7e1a46000 ---p 001c3000 08:04 32118997 /usr/lib64/libc-2.17.so
2ba7e1a46000-2ba7e1a4a000 r--p 001c2000 08:04 32118997 /usr/lib64/libc-2.17.so
2ba7e1a4a000-2ba7e1a4c000 rw-p 001c6000 08:04 32118997 /usr/lib64/libc-2.17.so
2ba7e1a4c000-2ba7e1a51000 rw-p 00000000 00:00 0
2ba7e1a51000-2ba7e1b52000 r-xp 00000000 08:04 32119005 /usr/lib64/libm-2.17.so
2ba7e1b52000-2ba7e1d51000 ---p 00101000 08:04 32119005 /usr/lib64/libm-2.17.so
2ba7e1d51000-2ba7e1d52000 r--p 00100000 08:04 32119005 /usr/lib64/libm-2.17.so
2ba7e1d52000-2ba7e1d53000 rw-p 00101000 08:04 32119005 /usr/lib64/libm-2.17.so
2ba7e1d53000-2ba7e1d5a000 r-xp 00000000 08:04 32119027 /usr/lib64/librt-2.17.so
2ba7e1d5a000-2ba7e1f59000 ---p 00007000 08:04 32119027 /usr/lib64/librt-2.17.so
2ba7e1f59000-2ba7e1f5a000 r--p 00006000 08:04 32119027 /usr/lib64/librt-2.17.so
2ba7e1f5a000-2ba7e1f5b000 rw-p 00007000 08:04 32119027 /usr/lib64/librt-2.17.so
2ba7e1f5b000-2ba7e1f5f000 r--p 00000000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1
2ba7e1f5f000-2ba7e1f71000 r-xp 00004000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1
2ba7e1f71000-2ba7e1f74000 r--p 00016000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1
2ba7e1f74000-2ba7e1f75000 r--p 00019000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1
2ba7e1f75000-2ba7e1f76000 rw-p 0001a000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1
2ba7e1f76000-2ba7e1f8d000 r-xp 00000000 08:04 32119023 /usr/lib64/libpthread-2.17.so
2ba7e1f8d000-2ba7e218c000 ---p 00017000 08:04 32119023 /usr/lib64/libpthread-2.17.so
2ba7e218c000-2ba7e218d000 r--p 00016000 08:04 32119023 /usr/lib64/libpthread-2.17.so
2ba7e218d000-2ba7e218e000 rw-p 00017000 08:04 32119023 /usr/lib64/libpthread-2.17.so
2ba7e218e000-2ba7e2192000 rw-p 00000000 00:00 0
2ba7e293f000-2ba7e2ac0000 rw-p 00000000 00:00 0
562cba3af000-562cba3b1000 r--p 00000000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread
562cba3b1000-562cba3e1000 r-xp 00002000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread
562cba3e1000-562cba3ed000 r--p 00032000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread
562cba3ed000-562cba3ee000 r--p 0003e000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread
562cba3ee000-562cba3ef000 rw-p 0003f000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread
562cba3ef000-562cba3f7000 rw-p 00000000 00:00 0
562cbab9c000-562cc3a43000 rw-p 00000000 00:00 0 [heap]
7ffc9e687000-7ffc9e6aa000 rw-p 00000000 00:00 0 [stack]
7ffc9e796000-7ffc9e798000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted
Can you point me to that Ath_genomic.gff file so I can check/debug this ? Also, I see this is a conda version of gffread, what does gffread --version show?
Yes, this is a conda version and gffread --version showed is '0.12.7'
Uploading Ath_genomic.gff.tar.gz…